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Latest improvements for QIAGEN CLC Main Workbench

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QIAGEN CLC Main Workbench 20.0.2

Release date: 2020-02-03

Improvements

  • Metadata associations are preserved when importing .zip files containing both metadata tables and associated data.
  • Various minor improvements

Bug fixes

  • Fixed an issue where data elements selected in the Navigation Area were sometimes incorrectly preselected when browsing for inputs in wizard steps of tools and workflows.
  • Fixed a bug that prevented installed workflows with configuration options and at least one locked input from being configured through the Workflow Manager
  • Fixed an issue where some plots, including volcano plots and scatter plots, sometimes showed an incorrect tooltip when hovering over a data point with the mouse.
  • Fixed an issue when workflows were run in the batch mode or using Iterate elements, where if two input elements with the same name but in different folders were selected from the Navigation Area, and the "Use organisation of input data" option was chosen, then the inputs were allocated to the same batch, even though the batch overview showed that they would be in different batches. Now, they will be allocated to different batches, as shown in the batch overview.

General information

NCBI plans to change their blast database folder structure in early February 2020. When that happens, the Download BLAST Databases tool of QIAGEN CLC Main Workbench 20.0.2, and future updates, will list the new, dbV5 blast databases for download. The Create Blast Database tool will continue to create dbV4 databases. Databases of either version can be searched using the blast programs included in QIAGEN CLC Genomics Main 20.x release line.

Advanced notice

The Reverse Sequence (legacy) will be removed in a future version of the software. The "Run in Batch Mode..." functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the "Batch" checkbox when selecting input data. If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.



QIAGEN CLC Main Workbench 20.0.1

Release date: 2020-01-15

Improvements

  • Import of Gene Ontology Annotation files now supports files including BOM encoding.
  • The hmmsearch program, used by Pfam Domain Search, is now 64-bit on all platforms. Previously a 32-bit version was distributed for use on macOS.
  • File information is now included when printing the data from the Element info view.

Bug fixes

  • Fixed a bug in the Primer Designer, where clicking on each potential primer starting position did not highlight the the primer region.
  • Fixed a bug where sequences could not be downloaded from NCBI through the 'Show BLAST Hit Table' view
  • Fixed a bug in the advanced filter of the table view of sequence lists, where days and months could not be matched with corresponding values in the "Modified" column.
  • Fixed a bug in Experiments where very long column group headers could cause an "out of memory" error on macOS.
  • Fixed an issue in the element history of a result generated by Extract Annotations, where the reference sequence track could appear to have been used for extracting annotations, even when it was not used.
  • Fixed a bug in workflows using control flow elements, where some outputs were not saved if the same output channel was connected directly to both an output element and to a Collect and Distribute element. This problem occurred if the combined lengths of the input filenames for a given run exceeded 250 characters, and batch units were defined on the basis of the organization of the input data.
  • Fixed a bug in workflows containing two Iterate elements connected to each other, where it was not possible to select a metadata column for the inner Iterate element in the batch configuration step of the workflow wizard if two or more connections were made from the output channel of that element.
  • Various minor bugfixes

Advanced notice

The Reverse Sequence (legacy) will be removed in a future version of the software. The "Run in Batch Mode..." functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the "Batch" checkbox when selecting input data. If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.



QIAGEN CLC Main Workbench 20.0

Release date: 2019-12-11

New features

Protein structure and homology
  • Generate Biomolecule A new tool available from the side panel of Molecule Projects allowing biomolecules to be generated or extracted based on symmetry information in PDB files.
  • Find and Model Structure A new tool that finds suitable protein structures for representing a given protein sequence. From the resulting table, a structure model (homology model) of the sequence can be created by one click using one of the found protein structures as template.
  • Download 3D Protein Structure Database A new tool for downloading a curated database containing sequences with known 3D structures obtained from the Protein Data Bank
  • Molecule structures in a Molecule Project can now be exported to a PDB format file.
  • Search for PDB Structures at NCBI is now available when running the Workbench in Viewing Mode.
Workflows
  • When launching workflows, batch units can now be defined using metadata, supplied either as a CLC medata table or by selecting an Excel format file containing information about the data.
  • Workflows with multiple inputs, where those inputs should be matched with each other, can now be launched in batch mode, making use of the ability to define batch units based on metadata. For example, a workflow where sets of reads should be mapped to different reference sequences can now be launched in batch mode.
  • Two new workflow elements have been introduced, Iterate and Collect and Distribute, which allow workflows to be designed where the execution of different parts of a workflow can be finely controlled. For example, using these elements, a single workflow can contain an analysis step that will be run once per sample, as well as elements that should only be run once for a set of samples.
  • Workflows now produce a Workflow Result Metadata table, which contain one row per output, with the relevant data element associated with that row. When launched in batch mode, the batch the row relates to is clearly indicated.
  • CLC sequence files not yet imported can be imported on the fly, as an initial action when a workflow is run, avoiding the need import such data prior to launching the workflow. This is mostly of relevance if sharing data with other sites.
Export
  • Reports can now be exported in PDF format.
  • When exporting to PDF, there is now an option to export the history of the report.
BLAST
  • A new option for the BLAST tool called Filter out redundant results, will when enabled cull HSPs on a per subject sequence basis by removing HSPs that are completely enveloped by another HSP.
  • The NCBI blast executables have been updated to version 2.9.0.
  • The option "Choose filter to mask low complexity regions" has been renamed to "Mask low complexity regions".

Improvements

Workflows
  • All installed workflows can now be updated in a single operation from the Workflow Manager using the new Update All Workflows button.
  • Placeholder-based naming of outputs in workflows can now be configured at a finer level: the {input} or {2} placeholder is now replaced by the name of the first workflow input by default. This can then be further configured to use the names of other inputs by specifying them by number after a colon in the placeholder. For example: {2:1,3} would be replaced by the names of workflow inputs number 1 and 3. Previously, a workflow output configured as {2} was replaced by a concatenation of all the workflow input names.
  • The listing of items in the "Add Element" dialog in the Workflow Editor has been made improved. Installed workflows in the workbench, and no longer matches texts in the tooltips of the tools.
  • When running a workflow configured to use reference data, the Reference Data Set selection step has been updated to show the list of preconfigured elements in the tooltip.
  • The "Export to PDF" tool can now be used in workflows to export reports in PDF format.
Performance improvements:
  • Saving analysis results to an SSD is now considerably faster.
  • The import of ZIP files has been improved: temporary objects are cleaned up during the import process, reducing the required disk space.
  • Moving and deleting many elements at once is now faster.
  • Emptying the Recycle bin now takes place in the background.
  • Messages from tools are no longer presented in the form of black bubbles in the Processes area. Messages are still writtent to the log.
  • There are general performance improvements in the following areas:
    • The Navigation Area
    • BLAST and Add attB Sites tools when using large sequence lists
    • Opening large protein sequences
    • Making BLAST databases where most sequences have the same name.
Import and export
  • When exporting to PDF, there is now an option to export the history of the report.
  • The CSV importer has been updated:
    • Values no longer need to be enclosed in quotation marks in the CSV file to be successfully imported.
    • Data values starting with a numeric character but also containing non-numeric characters are now interpreted as text. Such values were previously converted to numbers and then only imported up to the first non-numeric character.
  • The import of Nexus files has been updated to more closely match the format specifications.
  • When selecting files to import from an import/export directory on a QIAGEN CLC Genomics Server, right-clicking on a folder name now brings up a menu with the options: "Add the content of a directory" or "Add the full content (recursively) of a directory".
  • The "Excel 2010" and "Excel 97-2007" exporters now export NaN and +/-Infinity values to #N/A.
  • When importing multiple files using the Standard Import, the process ends with an error if at least one of the files failed to import. The details of which file failed and why can be seen in the log.
  • The GenBank exporter now replaces any spaces in annotation names with underscores.
Searching
Metadata related
Create Box Plot
  • Create Box Plot now calculates the median and percentile values in the same way as the "quantile" method in R.
  • Whiskers of boxplots now range from the lowest data point within 1.5 times the inter quartile range (IQR) of the lower quartile and the highest data point within 1.5 IQR of the upper quartile. Previously, they extended 1.5 times the length of the box (IQR).
Other improvements
  • Outputs of tools provided by plugins now include the plugin name and version in the element history.
  • A new option when right-clicking on a table cell, Edit | Copy Cell, allows individual cells to be copied to the clipboard. Previously only whole rows could be copied
  • Tool and workflow logs now display an "Elapsed time" column.
  • In the tree view of phylogenetic trees, the "Reset Tree Toplogy" button will now also uncollapse any collapsed nodes.
  • The name of a non-default workspace is now shown in the Workbench title bar.
  • The table view ("Show Table") of plots has been improved in the cases where multiple data series are shown in the plot. The table now includes all of the x values from all data series, instead of the x values from just the first data series. If a data series is missing a y value for a specific x value, than the entry in the table will be empty.
  • The maximum size of a plot in a report displayed in the Workbench has been increased too 800 pixels, and the width/height ratio has been changed from 2/3 to 1/2.
  • The ranking of search results in Quick Launch has been improved.
  • CLC URLs have been made more compact.
  • The icon for the sequence view has been changed for protein sequences, so it is possible to distinguish protein sequence views from nucleotide sequence views based on the icon.
  • In the Reference Data Management dialog, the "usable free space" is shown instead of the previous "free space".
  • In the Batch Rename tool, the option 'Replace part of the name' fields have changed from 'From' and 'To' to 'Replace' and 'With' for clarification.

Bug fixes

  • Fixed an issue affecting mac OS X setups with accessibility settings enabled, where the "Replace Selection with Sequence" functionality available from within the Cloning editor could fail with an error.
  • Fixed a bug where workflow installer files did not include the specified icon.

Changes

  • The Java version bundled with QIAGEN CLC Main Workbench 20.0 is Java 11, where we use the JRE from AdoptOpenJDK.
  • Using Local Search, searches for sequences with a specific length or length range now only returns individual sequence elements that meet the search requirements. Previously searches were also done within other types of elements, e.g. sequences lists, read mappings, etc.
  • The Help -> Tutorials menu item has been replaced with Help -> Online Tutorials, which opens the online tutorials in a browser.
  • The Reverse Sequence tool has been moved to the Legacy folder of the Workbench Toolbox and "(legacy") appended to its name. It will be removed in a future version of the software.

Plugin notes

New plugins
  • Navigation Tools Provides the functionality formerly provided by the Bookmark Navigator and Recent Items Navigator plugins.
  • SignalP and TMHMM Provides the functionality formerly provided by the SignalP and TMHMM plugins
Plugin retirements

The following plugins have been retired, with their functionality being provided by a new plugin:

  • Bookmark Navigator
  • Recent Items Navigator
  • SignalP
  • TMHMM

The following plugins have been retired and their functionality is no longer available through the QIAGEN CLC Main Workbench:

  • PPfold
  • TRANSFAC

Advanced notice

The Reverse Sequence (legacy) will be removed in a future version of the software. The "Run in Batch Mode..." functionality for installed workflows with multiple inputs will be retired in a future release. Workflows with multiple inputs can now be launched in batch mode by checking the "Batch" checkbox when selecting input data. If you are concerned about these proposed changes, please contact our Support team by emailing ts-bioinformatics@qiagen.com.